1
|
Keller BA, Laight BJ, Varette O, Broom A, Wedge MÈ, McSweeney B, Cemeus C, Petryk J, Lo B, Burns B, Nessim C, Ong M, Chica RA, Atkins HL, Diallo JS, Ilkow CS, Bell JC. Personalized oncology and BRAF K601N melanoma: model development, drug discovery, and clinical correlation. J Cancer Res Clin Oncol 2021; 147:1365-1378. [PMID: 33555379 DOI: 10.1007/s00432-021-03545-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 01/25/2021] [Indexed: 12/13/2022]
Abstract
PURPOSE Mutations in BRAF are the most prominent activating mutations in melanoma and are increasingly recognized in other cancers. There is currently no accepted treatment regimen for patients with mutant BRAFK601N melanoma, and the study of melanoma driven by BRAF mutations at the 601 locus is lacking due to a paucity of cellular model systems. Therefore, we sought to better understand the treatment and clinical approach to patients with mutant BRAFK601N melanoma and subsequently develop a novel personalized oncology platform for rare or treatment-refractory cancers. METHODS We developed and characterized the first patient-derived, naturally occurring BRAFK601N melanoma model, described herein as OHRI-MEL-13, and assessed efficacy using the Prestwick Chemical Library and select targeted therapeutics. RESULTS OHRI-MEL-13 exhibits loss of heterozygosity of BRAF, closely mimics the original tumor's gene expression profile, is tumorigenic in immune-deficient murine models, and is available for public accession through American Type Culture Collection. We present in silico modeling data, which illustrates the therapeutic failure of BRAFV600E-targeted therapies in BRAFK601N mutants. Our platform elucidated a unique role for MEK inhibition with cobimetinib, which resulted in short-term clinical success by reducing the metastatic burden. CONCLUSION Our model of BRAFK601N-activated melanoma was developed, thoroughly characterized, and made available for public accession. This model served to demonstrate the feasibility of a novel personalized oncology platform that could be optimized at an institutional level for rare variant or treatment-refractory cancers. We also demonstrate the clinical utility of monotherapy MEK inhibition in a case of BRAFK601N melanoma.
Collapse
Affiliation(s)
- Brian A Keller
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada.
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, K1H 8M5, Canada.
- Department of Pathology and Laboratory Medicine, The Ottawa Hospital, 501 Smyth Road, Ottawa, K1H 8L6, Canada.
| | - Brian J Laight
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada
| | - Oliver Varette
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, K1H 8M5, Canada
| | - Aron Broom
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie Private, Ottawa, K1N 6N5, Canada
| | - Marie-Ève Wedge
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, K1H 8M5, Canada
| | - Benjamin McSweeney
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada
| | - Catia Cemeus
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada
| | - Julia Petryk
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada
| | - Bryan Lo
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada
- Department of Pathology and Laboratory Medicine, The Ottawa Hospital, 501 Smyth Road, Ottawa, K1H 8L6, Canada
- Molecular Oncology Diagnostics Laboratory, The Ottawa Hospital, 501 Smyth Road, Ottawa, K1H 8L6, Canada
| | - Bruce Burns
- Department of Pathology and Laboratory Medicine, The Ottawa Hospital, 501 Smyth Road, Ottawa, K1H 8L6, Canada
| | - Carolyn Nessim
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada
- Division of General Surgery, The Ottawa Hospital, 501 Smyth Road, Ottawa, K1H 8L6, Canada
| | - Michael Ong
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada
- Division of Medical Oncology, The Ottawa Hospital, 501 Smyth Road, Ottawa, K1H 8L6, Canada
| | - Roberto A Chica
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie Private, Ottawa, K1N 6N5, Canada
| | - Harold L Atkins
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, K1H 8M5, Canada
- The Ottawa Hospital Blood and Marrow Transplant Program, The Ottawa Hospital, 501 Smyth Road, Ottawa, K1H 8L6, Canada
| | - Jean-Simon Diallo
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, K1H 8M5, Canada
| | - Carolina S Ilkow
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, K1H 8M5, Canada
| | - John C Bell
- Centre for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, K1H 8M5, Canada
| |
Collapse
|
2
|
Consoli F, Barbieri G, Picciolini M, Medicina D, Bugatti M, Tovazzi V, Liserre B, Zambelli C, Zorzi F, Berruti A, Giurisato E, Vermi W. A Rare Complex BRAF Mutation Involving Codon V600 and K601 in Primary Cutaneous Melanoma: Case Report. Front Oncol 2020; 10:1056. [PMID: 32754440 PMCID: PMC7367153 DOI: 10.3389/fonc.2020.01056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/27/2020] [Indexed: 01/09/2023] Open
Abstract
BRAF is one of the most common mutated kinases detected in human cancer, particularly in cases of primary cutaneous melanomas (PCM). Mutations of the BRAF proto-oncogene, at the p.V600 codon, has been detected in more than 50% of primary and metastatic melanoma cells in clinical samples. In addition to the most frequent BRAF p.V600E mutation, corresponding to the single base pair substitution c.1799T>A, rarer mutations, within and outside the V600 codon, have been described. Expectedly, BRAF and MEK inhibitors (or their combination) have been poorly explored as potential therapeutic strategies in metastatic melanomas harboring this rare mutation. By using a set of sequencing techniques and immunohistochemistry, this work reports the genomic and clinical features of two melanoma patients showing a rare complex mutation affecting codon V600 and K601 of the BRAF gene, leading to a V600E2; K601I change. Specifically, these two patients show a distinct clinical behavior and significantly differ in their responses to BRAF and MEK inhibitors. Indeed, although this treatment has proven to be effective and safe in both cases, the observed variability between the two patients resulted as a direct consequence of the baseline extent of brain involvement, intracranial treatment failure as well as on the PTEN status.
Collapse
Affiliation(s)
| | | | | | - Daniela Medicina
- Unit of Anatomic Pathology, Spedali Civili di Brescia, Brescia, Italy
| | - Mattia Bugatti
- Unit of Anatomic Pathology, Spedali Civili di Brescia, Brescia, Italy
| | - Valeria Tovazzi
- Unit of Medical Oncology, Spedali Civili di Brescia, Brescia, Italy
| | - Barbara Liserre
- Department of Pathology, Fondazione Poliambulanza, Brescia, Italy
| | - Claudia Zambelli
- Unit of Anatomic Pathology, Spedali Civili di Brescia, Brescia, Italy
| | - Fausto Zorzi
- Department of Pathology, Fondazione Poliambulanza, Brescia, Italy
| | - Alfredo Berruti
- Unit of Medical Oncology, Spedali Civili di Brescia, Brescia, Italy.,Department of Medical and Surgical Specialties, Radiological Sciences, and Public Health, University of Brescia, Brescia, Italy
| | - Emanuele Giurisato
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom.,Department of Biotechnology Chemistry and Pharmacy, University of Siena, Siena, Italy
| | - William Vermi
- Unit of Medical Oncology, Spedali Civili di Brescia, Brescia, Italy.,Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| |
Collapse
|
3
|
Ma W, Brodie S, Agersborg S, Funari VA, Albitar M. Significant Improvement in Detecting BRAF, KRAS, and EGFR Mutations Using Next-Generation Sequencing as Compared with FDA-Cleared Kits. Mol Diagn Ther 2018. [PMID: 28639239 PMCID: PMC5606956 DOI: 10.1007/s40291-017-0290-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Introduction We compared mutations detected in EGFR, KRAS, and BRAF genes using next-generation sequencing (NGS) and confirmed by Sanger sequencing with mutations that could be detected by FDA-cleared testing kits. Methods Paraffin-embedded tissue from 822 patients was tested for mutations in EGFR, KRAS, and BRAF by NGS. Sanger sequencing of hot spots was used with locked nucleic acid to increase sensitivity for specific hot-spot mutations. This included 442 (54%) lung cancers, 168 (20%) colorectal cancers, 29 (4%) brain tumors, 33 (4%) melanomas, 14 (2%) thyroid cancers, and 16% others (pancreas, head and neck, and cancer of unknown origin). Results were compared with the approved list of detectable mutations in FDA kits for EGFR, KRAS, and BRAF. Results Of the 101 patients with EGFR abnormalities as detected by NGS, only 58 (57%) were detectable by cobas v2 and only 35 (35%) by therascreen. Therefore, 42 and 65%, respectively, more mutations were detected by NGS, including two patients with EGFR amplification. Of the 117 patients with BRAF mutation detected by NGS, 62 (53%) mutations were within codon 600, detectable by commercial kits, but 55 (47%) of the mutations were outside codon V600, detected by NGS only. Of the 321 patients with mutations in KRAS detected by NGS, 284 (88.5%) had mutations detectable by therascreen and 300 (93.5%) had mutations detectable by cobas. Therefore, 11.5 and 6.5% additional KRAS mutations were detected by NGS, respectively. Conclusion NGS provides significantly more comprehensive testing for mutations as compared with FDA-cleared kits currently available commercially.
Collapse
Affiliation(s)
- Wanlong Ma
- NeoGenomics Laboratories, 31 Columbia, Aliso Viejo, CA, 92656, USA
| | - Steven Brodie
- NeoGenomics Laboratories, 31 Columbia, Aliso Viejo, CA, 92656, USA
| | - Sally Agersborg
- NeoGenomics Laboratories, 31 Columbia, Aliso Viejo, CA, 92656, USA
| | - Vincent A Funari
- NeoGenomics Laboratories, 31 Columbia, Aliso Viejo, CA, 92656, USA
| | - Maher Albitar
- NeoGenomics Laboratories, 31 Columbia, Aliso Viejo, CA, 92656, USA.
| |
Collapse
|
4
|
BRAF-inhibitors can exert control of disease in BRAF T599I mutated melanoma: a case report. Melanoma Res 2018; 28:143-146. [DOI: 10.1097/cmr.0000000000000417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
5
|
Richtig G, Hoeller C, Kashofer K, Aigelsreiter A, Heinemann A, Kwong L, Pichler M, Richtig E. Beyond the BRAF
V
600E
hotspot: biology and clinical implications of rare BRAF
gene mutations in melanoma patients. Br J Dermatol 2017; 177:936-944. [DOI: 10.1111/bjd.15436] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2017] [Indexed: 12/15/2022]
Affiliation(s)
- G. Richtig
- Institute of Experimental and Clinical Pharmacology; Medical University of Graz; Graz Austria
- Department of Dermatology; Medical University of Graz; Graz Austria
| | - C. Hoeller
- Department of Dermatology; Medical University of Vienna; Vienna Austria
| | - K. Kashofer
- Institute for Pathology; Medical University of Graz; Graz Austria
| | - A. Aigelsreiter
- Institute for Pathology; Medical University of Graz; Graz Austria
| | - A. Heinemann
- Institute of Experimental and Clinical Pharmacology; Medical University of Graz; Graz Austria
| | - L.N. Kwong
- Translational Molecular Pathology; The University of Texas MD Anderson Cancer Center; Houston TX U.S.A
| | - M. Pichler
- Division of Oncology; Medical University of Graz; Graz Austria
- Department of Experimental Therapeutics; The University of Texas MD Anderson Cancer Center; Houston TX U.S.A
| | - E. Richtig
- Department of Dermatology; Medical University of Graz; Graz Austria
| |
Collapse
|
6
|
Yang Y, Shen X, Li R, Shen J, Zhang H, Yu L, Liu B, Wang L. The detection and significance of EGFR and BRAF in cell-free DNA of peripheral blood in NSCLC. Oncotarget 2017; 8:49773-49782. [PMID: 28572536 PMCID: PMC5564806 DOI: 10.18632/oncotarget.17937] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 05/04/2017] [Indexed: 01/23/2023] Open
Abstract
OBJECTIVE Although driver mutation status is crucial to targeted therapy decision-making in non-small cell lung cancer (NSCLC), due to unavailable or inadequate biopsies, there are still many patients with unknown mutation status. A promising way to solve this problem is liquid biopsy, such as cell-free DNA (cfDNA) in peripheral blood. Additionally, due to the little amount of cfDNA, detecting methods with high sensitivity, specificity and economy are required in clinical practice. Here, we explored the feasibility of Competitive Allele-Specific TaqMan® PCR (CastPCR) detecting driver mutations in cfDNA from plasma in lung adenocarcinoma patients. RESULTS Sensitivity, specificity, concordance, PPV and NPV of CastPCR detecting EGFR mutations in cfDNA was 56.4% (31/55), 94.2% (49/52), 74.8% (80/107), 91.2% (31/34) and 67.1% (49/73), respectively. Notably, specificity and PPV for p.T790M both reached 100.0%. For BRAF detection, it was 28.6% (2/7), 93.0% (93/100), 88.8% (95/107), 22.2% (2/9) and 94.9% (93/98), respectively. MATERIALS AND METHODS Plasma specimens of 107 lung adenocarcinoma patients and their matched tumor formalin fixed paraffin embedded (FFPE) samples were analyzed. CastPCR was used to detect EGFR (c.2235_2249del, c.2236_2250del, c.2369C>T p.T790M, c.2573T>G p.L858R) and BRAF (c.1406G>C p.G469A, c.1799T>A p.V600E, c.1781A>G p.D594G) mutations. Mutation results of tumor tissue was set as gold standard, and the sensitivity, specificity, concordance, positive predictive value (PPV) and negative predictive value (NPV) were calculated for each mutation. CONCLUSIONS For patients whose tumor tissue is unavailable or inadequate, EGFR mutation detection in cfDNA with CastPCR could be first choice. Mutation positive results may provide reference for further clinical medication. While negative results indicate that detection in tissue should be considered as the following step. In this way, tumor tissue could be economized to the maximum extent and the risk of repeated percutaneous transthoracic lung biopsy could also be lowered to the maximum extent. For BRAF detection in cfDNA, CastPCR is a specific method while the sensitivity needs further exploration.
Collapse
Affiliation(s)
- Yang Yang
- The Comprehensive Cancer Center of Drum Tower Hospital, Nanjing University Medical School and Clinical Cancer Institute of Nanjing University, Nanjing 210008, PR China
- Nanjing Xianlin Drum Tower Hospital, Nanjing 210046, PR China
| | - Xiaoyan Shen
- The Comprehensive Cancer Center of Drum Tower Hospital, Nanjing University Medical School and Clinical Cancer Institute of Nanjing University, Nanjing 210008, PR China
| | - Rutian Li
- The Comprehensive Cancer Center of Drum Tower Hospital, Nanjing University Medical School and Clinical Cancer Institute of Nanjing University, Nanjing 210008, PR China
| | - Jie Shen
- The Comprehensive Cancer Center of Drum Tower Hospital, Nanjing University Medical School and Clinical Cancer Institute of Nanjing University, Nanjing 210008, PR China
| | - Hang Zhang
- The Comprehensive Cancer Center of Drum Tower Hospital, Nanjing University Medical School and Clinical Cancer Institute of Nanjing University, Nanjing 210008, PR China
| | - Lixia Yu
- The Comprehensive Cancer Center of Drum Tower Hospital, Nanjing University Medical School and Clinical Cancer Institute of Nanjing University, Nanjing 210008, PR China
| | - Baorui Liu
- The Comprehensive Cancer Center of Drum Tower Hospital, Nanjing University Medical School and Clinical Cancer Institute of Nanjing University, Nanjing 210008, PR China
| | - Lifeng Wang
- The Comprehensive Cancer Center of Drum Tower Hospital, Nanjing University Medical School and Clinical Cancer Institute of Nanjing University, Nanjing 210008, PR China
| |
Collapse
|
7
|
Richtig G, Richtig E, Kashofer K, Koch L, Winter G, Hoefler G, Pichler M, Ehall B, Grübler MR, Heinemann A, Aigelsreiter A. Testing and clinical implications for non-V600 BRAF mutations in metastatic NRAS mt melanoma. Br J Dermatol 2017; 177:860-861. [PMID: 27925152 DOI: 10.1111/bjd.15222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- G Richtig
- Institute of Experimental and Clinical Pharmacology, Medical University of Graz, Graz, Austria.,Department of Dermatology, Medical University of Graz, Graz, Austria
| | - E Richtig
- Department of Dermatology, Medical University of Graz, Graz, Austria
| | - K Kashofer
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | - L Koch
- Department of Dermatology, Medical University of Graz, Graz, Austria
| | - G Winter
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | - G Hoefler
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | - M Pichler
- Division of Oncology, Medical University of Graz, Graz, Austria
| | - B Ehall
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | - M R Grübler
- Swiss Cardiovascular Center Bern, Department of Cardiology, Bern University Hospital, Bern, Switzerland.,Department of Internal Medicine (Division of Endocrinology and Diabetology), Medical University of Graz, Graz, Austria
| | - A Heinemann
- Institute of Experimental and Clinical Pharmacology, Medical University of Graz, Graz, Austria
| | - A Aigelsreiter
- Institute of Pathology, Medical University of Graz, Graz, Austria
| |
Collapse
|
8
|
Richtig G, Aigelsreiter A, Kashofer K, Talakic E, Kupsa R, Schaider H, Richtig E. Two Case Reports of Rare BRAF Mutations in Exon 11 and Exon 15 with Discussion of Potential Treatment Options. Case Rep Oncol 2016; 9:543-546. [PMID: 27790118 PMCID: PMC5075727 DOI: 10.1159/000449125] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
BRAF mutations occur in up to 50% of melanomas. Mutations in the BRAF gene directly influence the patient's treatment because several inhibitors are available that only target BRAFV600 mutations. Herein, we describe two cases of patients with metastatic melanomas, each carrying a ‘nonstandard’ mutation in the BRAF gene: BRAFK601E and BRAFG466E, respectively. The first patient was treated with a MEK inhibitor and the second one with ipilimumab. However, not all BRAF mutations result in increased BRAF kinase activity, and clinical data for ‘nonstandard’ mutations, such as those described in our case report, are sparse. Therefore, treatment with MEK inhibitors can be helpful in cases where BRAF mutations result in increased activity, whereas immune checkpoint inhibitors might be used in cases where the mutations lead to activity levels below those of the wild type.
Collapse
Affiliation(s)
- Georg Richtig
- Department of Dermatology, Medical University of Graz, Graz, Austria; Institute of Experimental and Clinical Pharmacology, Medical University of Graz, Graz, Austria
| | | | - Karl Kashofer
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Emina Talakic
- Division of General Radiological Diagnostics, Department of Radiology, Medical University of Graz, Graz, Austria
| | - Romana Kupsa
- Department of Dermatology, Medical University of Graz, Graz, Austria
| | - Helmut Schaider
- Dermatology Research Centre, School of Medicine, The University of Queensland, Brisbane, Qld., Australia
| | - Erika Richtig
- Department of Dermatology, Medical University of Graz, Graz, Austria
| |
Collapse
|
9
|
Yee SS, Lieberman DB, Blanchard T, Rader J, Zhao J, Troxel AB, DeSloover D, Fox AJ, Daber RD, Kakrecha B, Sukhadia S, Belka GK, DeMichele AM, Chodosh LA, Morrissette JJD, Carpenter EL. A novel approach for next-generation sequencing of circulating tumor cells. Mol Genet Genomic Med 2016; 4:395-406. [PMID: 27468416 PMCID: PMC4947859 DOI: 10.1002/mgg3.210] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 02/16/2016] [Accepted: 02/01/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) of surgically resected solid tumor samples has become integral to personalized medicine approaches for cancer treatment and monitoring. Liquid biopsies, or the enrichment and characterization of circulating tumor cells (CTCs) from blood, can provide noninvasive detection of evolving tumor mutations to improve cancer patient care. However, the application of solid tumor NGS approaches to circulating tumor samples has been hampered by the low-input DNA available from rare CTCs. Moreover, whole genome amplification (WGA) approaches used to generate sufficient input DNA are often incompatible with blood collection tube preservatives used to facilitate clinical sample batching. METHODS To address this, we have developed a novel approach combining tumor cell isolation from preserved blood with Repli-G WGA and Illumina TruSeq Amplicon Cancer Panel-based NGS. We purified cell pools ranging from 10 to 1000 cells from three different cell lines, and quantitatively demonstrate comparable quality of DNA extracted from preserved versus unpreserved samples. RESULTS Preservation and WGA were compatible with the generation of high-quality libraries. Known point mutations and gene amplification were detected for libraries that had been prepared from amplified DNA from preserved blood. CONCLUSION These spiking experiments provide proof of concept of a clinically applicable workflow for real-time monitoring of patient tumor using noninvasive liquid biopsies.
Collapse
Affiliation(s)
- Stephanie S. Yee
- Department of MedicineUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPennsylvania
| | - David B. Lieberman
- Department of Pathology and Laboratory MedicineHospital of the University of PennsylvaniaPhiladelphiaPennsylvania
| | - Tatiana Blanchard
- Department of Cancer BiologyUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPennsylvania
- Abramson Family Cancer Research InstituteUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPennsylvania
| | - JulieAnn Rader
- Division of OncologyCenter for Childhood Cancer ResearchChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvania
| | - Jianhua Zhao
- Department of Pathology and Laboratory MedicineHospital of the University of PennsylvaniaPhiladelphiaPennsylvania
| | - Andrea B. Troxel
- Center for Clinical Epidemiology and BiostatisticsUniversity of PennsylvaniaPhiladelphiaPennsylvania
- Abramson Cancer CenterUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPennsylvania
| | - Daniel DeSloover
- Department of Pathology and Laboratory MedicineHospital of the University of PennsylvaniaPhiladelphiaPennsylvania
| | - Alan J. Fox
- Department of Pathology and Laboratory MedicineHospital of the University of PennsylvaniaPhiladelphiaPennsylvania
| | - Robert D. Daber
- Department of Pathology and Laboratory MedicineHospital of the University of PennsylvaniaPhiladelphiaPennsylvania
| | - Bijal Kakrecha
- Department of MedicineUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPennsylvania
| | - Shrey Sukhadia
- Department of Pathology and Laboratory MedicineHospital of the University of PennsylvaniaPhiladelphiaPennsylvania
| | - George K. Belka
- Department of Cancer BiologyUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPennsylvania
- Abramson Family Cancer Research InstituteUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPennsylvania
| | - Angela M. DeMichele
- Department of MedicineUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPennsylvania
- Abramson Cancer CenterUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPennsylvania
| | - Lewis A. Chodosh
- Department of MedicineUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPennsylvania
- Department of Cancer BiologyUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPennsylvania
- Abramson Family Cancer Research InstituteUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPennsylvania
| | - Jennifer J. D. Morrissette
- Department of Pathology and Laboratory MedicineHospital of the University of PennsylvaniaPhiladelphiaPennsylvania
| | - Erica L. Carpenter
- Department of MedicineUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPennsylvania
- Abramson Cancer CenterUniversity of Pennsylvania Perelman School of MedicinePhiladelphiaPennsylvania
| |
Collapse
|
10
|
Detection of BRAF Mutations Using a Fully Automated Platform and Comparison with High Resolution Melting, Real-Time Allele Specific Amplification, Immunohistochemistry and Next Generation Sequencing Assays, for Patients with Metastatic Melanoma. PLoS One 2016; 11:e0153576. [PMID: 27111917 PMCID: PMC4844167 DOI: 10.1371/journal.pone.0153576] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/31/2016] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Metastatic melanoma is a severe disease with one of the highest mortality rate in skin diseases. Overall survival has significantly improved with immunotherapy and targeted therapies. Kinase inhibitors targeting BRAF V600 showed promising results. BRAF genotyping is mandatory for the prescription of anti-BRAF therapies. METHODS Fifty-nine formalin-fixed paraffin-embedded melanoma samples were assessed using High-Resolution-Melting (HRM) PCR, Real-time allele-specific amplification (RT-ASA) PCR, Next generation sequencing (NGS), immunohistochemistry (IHC) and the fully-automated molecular diagnostics platform IdyllaTM. Sensitivity, specificity, positive predictive value and negative predictive value were calculated using NGS as the reference standard to compare the different assays. RESULTS BRAF mutations were found in 28(47.5%), 29(49.2%), 31(52.5%), 29(49.2%) and 27(45.8%) samples with HRM, RT-ASA, NGS, IdyllaTM and IHC respectively. Twenty-six (81.2%) samples were found bearing a c.1799T>A (p.Val600Glu) mutation, three (9.4%) with a c.1798_1799delinsAA (p.Val600Lys) mutation and one with c.1789_1790delinsTC (p.Leu597Ser) mutation. Two samples were found bearing complex mutations. CONCLUSIONS HRM appears the less sensitive assay for the detection of BRAF V600 mutations. The RT-ASA, IdyllaTM and IHC assays are suitable for routine molecular diagnostics aiming at the prescription of anti-BRAF therapies. IdyllaTM assay is fully-automated and requires less than 2 minutes for samples preparation and is the fastest of the tested assays.
Collapse
|
11
|
Building a Robust Tumor Profiling Program: Synergy between Next-Generation Sequencing and Targeted Single-Gene Testing. PLoS One 2016; 11:e0152851. [PMID: 27043212 PMCID: PMC4820127 DOI: 10.1371/journal.pone.0152851] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 03/21/2016] [Indexed: 12/25/2022] Open
Abstract
Next-generation sequencing (NGS) is a powerful platform for identifying cancer mutations. Routine clinical adoption of NGS requires optimized quality control metrics to ensure accurate results. To assess the robustness of our clinical NGS pipeline, we analyzed the results of 304 solid tumor and hematologic malignancy specimens tested simultaneously by NGS and one or more targeted single-gene tests (EGFR, KRAS, BRAF, NPM1, FLT3, and JAK2). For samples that passed our validated tumor percentage and DNA quality and quantity thresholds, there was perfect concordance between NGS and targeted single-gene tests with the exception of two FLT3 internal tandem duplications that fell below the stringent pre-established reporting threshold but were readily detected by manual inspection. In addition, NGS identified clinically significant mutations not covered by single-gene tests. These findings confirm NGS as a reliable platform for routine clinical use when appropriate quality control metrics, such as tumor percentage and DNA quality cutoffs, are in place. Based on our findings, we suggest a simple workflow that should facilitate adoption of clinical oncologic NGS services at other institutions.
Collapse
|